Merge pull request #1 from Exabyte-io/feature/SOF-6013

Feature/sof 6013

Author: azech-hqs

README.md

@@ -1,12 +1,70 @@
-# template-definitions
+[![npm version](https://badge.fury.io/js/%40exabyte-io%2Fade.js.svg)](https://badge.fury.io/js/%40exabyte-io%2Fade.js)
+[![License: Apache](https://img.shields.io/badge/License-Apache-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0)
 
-Template repository for entity definition libraries in Javascript
+# ade.js
 
-See [here](https://docs.github.com/en/github-ae@latest/repositories/creating-and-managing-repositories/creating-a-repository-from-a-template)
-for details on how to use this repository.
+ade.js houses entity definitions for use in the Mat3ra platform.
 
-Included is a simple `template.py` analog to `cookiecutter` which will prompt
-the user for some information and then write out templated values in select files.
-After usage, the `template.py` file can be removed and the `README.md` and associated
-`files` can be committed.
 
+### Installation
+
+For usage within a javascript project:
+
+```bash
+npm install @exabyte-io/ade.js
+```
+
+For development:
+
+```bash
+git clone https://github.com/Exabyte-io/ade.js.git
+```
+
+
+### Contribution
+
+This repository is an [open-source](LICENSE.md) work-in-progress and we welcome contributions.
+
+We regularly deploy the latest code containing all accepted contributions online as part of the
+[Mat3ra.com](https://mat3ra.com) platform, so contributors will see their code in action there.
+
+See [ESSE](https://github.com/Exabyte-io/esse) for additional context regarding the data schemas used here.
+
+Useful commands for development:
+
+```bash
+# run linter without persistence
+npm run lint
+
+# run linter and save edits
+npm run lint:fix
+
+# compile the library
+npm run transpile
+
+# run tests
+npm run test
+```
+
+ADe
+===
+
+The`ADe` package sits just below the `WoDe` package in the Mat3ra workflow
+ecosystem, where `ADe` houses entity definitions for:
+
+- `Application` - uniquely determined by `name, [version], [build]`
+- `Executable` - defined for a given application and accessible from application by name
+- `Flavor` - defined for a given executable and accessible from executable by name
+- `Template` - a jinja template for an application input file
+
+The relevant data parameterizing these entities is housed in
+the [Application Flavors](https://github.com/Exabyte-io/exabyte-application-flavors)
+repository. This includes the supported applications, executables, flavors,
+and defined templates.
+
+Templates themselves are organized by application in a top-level `assets`
+directory in `application-flavors` and the API for loading and working with templates can be found in
+each application's `assets.js` module.
+At build time, all templates are loaded and compiled into a single monolithic
+JS file using `build_templates.js` so that it can be used in the client as well as in NodeJS.
+This is how templates are consumed from `applicaton-flavors` in `ADe`.

package-lock.json

@@ -1,7 +1,7 @@
 {
-    "name": "@exabyte-io/PROJECT_NAME",
+    "name": "@exabyte-io/ade.js",
     "version": "0.0.0",
-    "description": "PROJECT_DESCRIPTION",
+    "description": "Application DEfinitions",
     "scripts": {
         "test": "nyc --reporter=text mocha --recursive --bail --require @babel/register/lib --require tests/setup.js tests",
         "lint": "eslint src tests && prettier --write src tests",
@@ -13,7 +13,7 @@
     },
     "repository": {
         "type": "git",
-        "url": "https://github.com/Exabyte-io/PROJECT_NAME.git"
+        "url": "https://github.com/Exabyte-io/ade.js.git"
     },
     "main": "dist/index.js",
     "files": [
@@ -23,10 +23,10 @@
     ],
     "author": "Exabyte Inc.",
     "bugs": {
-        "url": "https://github.com/Exabyte-io/PROJECT_NAME/issues"
+        "url": "https://github.com/Exabyte-io/ade.js/issues"
     },
     "license": "Apache-2.0",
-    "homepage": "https://github.com/Exabyte-io/PROJECT_NAME",
+    "homepage": "https://github.com/Exabyte-io/ade.js",
     "dependencies": {
         "@babel/cli": "7.16.0",
         "@babel/core": "7.16.0",
@@ -35,7 +35,16 @@
         "@babel/preset-env": "7.16.4",
         "@babel/preset-react": "7.16.7",
         "@babel/register": "^7.16.0",
-        "@babel/runtime-corejs3": "7.16.8"
+        "@babel/runtime-corejs3": "7.16.8",
+        "@exabyte-io/application-flavors.js": "2022.7.24-0",
+        "@exabyte-io/code.js": "2022.7.19-0",
+        "@exabyte-io/made.js": "2022.6.15-0",
+        "@exabyte-io/periodic-table.js": "2022.6.8-0",
+        "lodash": "^4.17.21",
+        "mixwith": "^0.1.1",
+        "swig": "^1.4.2",
+        "underscore": "^1.13.3",
+        "underscore.string": "^3.3.4"
     },
     "devDependencies": {
         "chai": "^4.3.4",
@@ -62,4 +71,3 @@
         "*.{js,css}": "prettier --write"
     }
 }
-

package.json

@@ -0,0 +1,114 @@
+import lodash from "lodash";
+import { getAppTree, getAppData, allApplications } from "@exabyte-io/application-flavors.js";
+import { NamedDefaultableInMemoryEntity } from "@exabyte-io/code.js/dist/entity";
+
+import { Executable } from "./executable";
+import { getApplicationConfig, getExecutableConfig } from "./tree";
+
+
+export class Application extends NamedDefaultableInMemoryEntity {
+    static Executable = Executable;
+
+    constructor(config) {
+        const staticConfig = getApplicationConfig(config);
+        super({...staticConfig, ...config});
+    }
+
+    // TODO: extract this from application-flavors "global" default config for espresso 5.4.0
+    static get defaultConfig() {
+        return {
+            name: 'espresso',
+            shortName: 'qe',
+            version: '5.4.0',
+            summary: 'Quantum Espresso',
+            build: 'Default',
+        }
+    }
+
+    static create(config) {
+        return this.createFromNameVersionBuild(config);
+    }
+
+    static createFromNameVersionBuild({name, version = null, build = "Default"}) {
+        return new Application({name, version, build});
+    }
+
+    getExecutables() {
+        return this.executables;
+    }
+
+    getBuilds() {
+        const data = getAppData(this.prop("name"));
+        const {versions} = data;
+        const builds = ["Default"];
+        versions.map((v) => v.build && builds.push(v.build));
+        return lodash.uniq(builds);
+    }
+
+    getVersions() {
+        const data = getAppData(this.prop("name"));
+        const {versions} = data;
+        const these = versions.map((v) => v.version);
+        return lodash.uniq(these);
+    }
+
+    static getUniqueAvailableNames() {
+        return allApplications;
+    }
+
+    getExecutableByName(name = null) {
+        return new this.constructor.Executable(
+            getExecutableConfig({
+                appName: this.prop("name"),
+                execName: name,
+            })
+        );
+    }
+
+    getExecutableByConfig(config) {
+        return config ? this.getExecutableByName(config.name) : this.defaultExecutable;
+    }
+
+    get defaultExecutable() {
+        return this.getExecutableByName();
+    }
+
+    // override upon inheritance
+    get allowedModelTypes() {
+        return []
+    }
+
+    get summary() {
+        return this.prop("summary");
+    }
+
+    get version() {
+        return this.prop("version");
+    }
+
+    get build() {
+        return this.prop("build");
+    }
+
+    get shortName() {
+        return this.prop("shortName", this.prop("name"));
+    }
+
+    get executables() {
+        const tree = getAppTree(this.prop("name"));
+        return Object.keys(tree).map(key => {
+            return new this.constructor.Executable(
+                Object.assign({}, tree[key], {name: key})
+            )
+        })
+    }
+
+    get hasAdvancedComputeOptions() {
+        return this.prop("hasAdvancedComputeOptions");
+    }
+
+    get isLicensed() {
+        return this.prop("isLicensed");
+    }
+
+}

src/application.js

@@ -0,0 +1,4 @@
+export { NWChemTotalEnergyContextProvider } from "./context/providers/nwchem/providers";
+export { QEPWXContextProvider, QENEBContextProvider } from "./context/providers/espresso/providers";
+export { VASPContextProvider, VASPNEBContextProvider } from "./context/providers/vasp/providers";
+export { ExecutableContextProvider } from "./context/providers"

src/context.js

@@ -0,0 +1,10 @@
+import { ContextProvider } from "@exabyte-io/code.js/dist/context";
+
+export class ExecutableContextProvider extends ContextProvider {
+    constructor(config) {
+        super({
+            ...config,
+            domain: "executable"
+        });
+    }
+}

src/context/providers.js

@@ -0,0 +1,112 @@
+import _ from "underscore";
+import lodash from "lodash";
+import { mix } from "mixwith";
+import s from "underscore.string";
+
+import { Made } from "@exabyte-io/made.js";
+import { PERIODIC_TABLE } from "@exabyte-io/periodic-table.js";
+
+import {
+    MaterialContextMixinBuilder,
+    MaterialsContextMixinBuilder,
+    MaterialsSetContextMixin,
+    MethodDataContextMixin,
+    WorkflowContextMixin,
+    JobContextMixin
+} from "@exabyte-io/code.js/dist/context";
+import { ExecutableContextProvider } from "../../providers";
+
+export class QEPWXContextProvider extends mix(ExecutableContextProvider).with(
+    MaterialContextMixinBuilder(Made.Material),
+    MethodDataContextMixin,
+    WorkflowContextMixin,
+    JobContextMixin,
+) {
+
+    get atomSymbols() {return this.material.Basis.uniqueElements}
+
+    get atomicPositionsWithoutConstraints() {return this.material.Basis.atomicPositions}
+
+    get atomicPositions() {return this.material.Basis.atomicPositionsWithConstraints};
+
+    /*
+     * @NOTE: Overriding getData makes this provider "stateless", ie. delivering data from scratch each time and not
+     *        considering the content of `this.data`, and `this.isEdited` field(s).
+     */
+    getData() {
+
+        // the below values are read from PlanewaveDataManager instead
+        // ECUTWFC = 40;
+        // ECUTRHO = 200;
+
+        const IBRAV = 0;
+
+        return {
+            IBRAV,
+            RESTART_MODE: this.RESTART_MODE,
+            NAT: this.atomicPositions.length,
+            NTYP: this.atomSymbols.length,
+            ATOMIC_POSITIONS: this.atomicPositions.join('\n'),
+            ATOMIC_POSITIONS_WITHOUT_CONSTRAINTS: this.atomicPositionsWithoutConstraints.join('\n'),
+            CELL_PARAMETERS: this.CELL_PARAMETERS,
+            ATOMIC_SPECIES: this.ATOMIC_SPECIES,
+        }
+    }
+
+    get RESTART_MODE() {
+        return (this.job.parentJob || this.workflow.hasRelaxation) ? 'restart' : 'from_scratch';
+    }
+
+    getPseudoBySymbol(symbol) {
+        return (this.methodData.pseudo || []).find(p => p.element === symbol);
+    }
+
+    get ATOMIC_SPECIES() {
+        // atomic species with pseudopotentials
+        return _.map(this.atomSymbols, (symbol) => {
+            const pseudo = this.getPseudoBySymbol(symbol);
+            return QEPWXContextProvider.symbolToAtomicSpecie(symbol, pseudo);
+        }).join('\n');
+    }
+
+    get CELL_PARAMETERS() {
+        return this.material.Lattice.vectorArrays.map(x => {
+            return x.map(y => {
+                return s.sprintf('%14.9f', y).trim();
+            }).join(' ');
+        }).join('\n');
+
+    }
+
+    static symbolToAtomicSpecie(symbol, pseudo) {
+        const el = PERIODIC_TABLE[symbol];
+        const filename = pseudo ? lodash.get(pseudo, 'filename', s.strRightBack(pseudo.path, '/')) : '';
+        return el ? s.sprintf('%s %f %s', symbol, el.atomic_mass, filename) : undefined;
+    }
+}
+
+export class QENEBContextProvider extends mix(ExecutableContextProvider).with(
+    MaterialContextMixinBuilder(Made.Material),
+    MaterialsContextMixinBuilder(Made.Material),
+    MaterialsSetContextMixin,
+    MethodDataContextMixin,
+    WorkflowContextMixin,
+    JobContextMixin,
+) {
+
+    getData() {
+        const sortedMaterials = this.sortMaterialsByIndexInSet(this.materials);
+        const PWXContexts = sortedMaterials.map(material => {
+            const context = Object.assign({}, this.config.context, {material: material});
+            const config = Object.assign({}, this.config, {context});
+            return new QEPWXContextProvider(config).getData();
+        });
+
+        return {
+            ..._.omit(PWXContexts[0], ["ATOMIC_POSITIONS", "ATOMIC_POSITIONS_WITHOUT_CONSTRAINTS"]),
+            FIRST_IMAGE: PWXContexts[0].ATOMIC_POSITIONS,
+            LAST_IMAGE: PWXContexts[PWXContexts.length - 1].ATOMIC_POSITIONS,
+            INTERMEDIATE_IMAGES: PWXContexts.slice(1, PWXContexts.length - 1).map(data => data.ATOMIC_POSITIONS),
+        }
+    }
+}